SMTL ID : 1mxf.1

Crystal Structure of Inhibitor Complex of Putative Pteridine Reductase 2 (PTR2) from Trypanosoma cruzi

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-tetramer

Ligands

4 x NDP: NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE(Non-covalent)

NDP.1: 30 residues within 4Å: Chain A: G.18, R.21, R.22, I.23, H.41, Y.42, R.43, H.44, S.45, G.69, D.70, L.71, S.72, N.101, A.102, S.103, A.104, E.131, S.135, L.167, C.168, D.169, Y.182, K.186, P.212, G.213, L.214, S.215, L.216 Ligands: MTX.2 27 PLIP interactions: 27 interactions with chain A Hydrophobic interactions: A:P.212 Hydrogen bonds: A:G.18, A:R.22, A:I.23, A:R.43, A:R.43, A:H.44, A:S.45, A:L.71, A:S.72, A:N.101, A:S.103, A:S.103, A:S.103, A:E.131, A:K.186, A:S.215, A:L.216 Water bridges: A:R.43, A:N.101, A:N.101, A:S.103 Salt bridges: A:R.21, A:R.22, A:R.22, A:R.43 pi-Cation interactions: A:R.43 NDP.3: 29 residues within 4Å: Chain B: G.18, R.22, I.23, H.41, Y.42, R.43, H.44, S.45, G.69, D.70, L.71, S.72, N.101, A.102, S.103, A.104, E.131, S.135, L.167, C.168, D.169, Y.182, K.186, P.212, G.213, L.214, S.215, L.216 Ligands: MTX.4 28 PLIP interactions: 28 interactions with chain B Hydrophobic interactions: B:P.212 Hydrogen bonds: B:G.18, B:R.22, B:I.23, B:R.43, B:R.43, B:H.44, B:S.45, B:D.70, B:L.71, B:S.72, B:N.101, B:S.103, B:S.103, B:S.103, B:Y.182, B:K.186, B:S.215, B:L.216 Water bridges: B:A.20, B:G.24, B:R.43, B:N.101, B:S.103 Salt bridges: B:R.22, B:R.22, B:R.43 pi-Cation interactions: B:R.43 NDP.5: 30 residues within 4Å: Chain C: G.18, R.21, R.22, I.23, H.41, Y.42, R.43, H.44, S.45, G.69, D.70, L.71, S.72, N.101, A.102, S.103, A.104, E.131, S.135, L.167, C.168, D.169, Y.182, K.186, P.212, G.213, L.214, S.215, L.216 Ligands: MTX.6 29 PLIP interactions: 29 interactions with chain C Hydrophobic interactions: C:P.212 Hydrogen bonds: C:R.21, C:R.22, C:I.23, C:R.43, C:R.43, C:H.44, C:S.45, C:D.70, C:L.71, C:S.72, C:N.101, C:S.103, C:S.103, C:S.103, C:E.131, C:K.186, C:S.215, C:L.216 Water bridges: C:A.20, C:R.22, C:G.24, C:N.101, C:S.103 Salt bridges: C:R.22, C:R.22, C:R.43 pi-Cation interactions: C:R.43, C:R.43 NDP.7: 30 residues within 4Å: Chain D: G.18, R.21, R.22, I.23, H.41, Y.42, R.43, H.44, S.45, G.69, D.70, L.71, S.72, N.101, A.102, S.103, A.104, E.131, S.135, L.167, C.168, D.169, Y.182, K.186, P.212, G.213, L.214, S.215, L.216 Ligands: MTX.8 28 PLIP interactions: 28 interactions with chain D Hydrophobic interactions: D:P.212 Hydrogen bonds: D:G.18, D:R.21, D:R.22, D:I.23, D:R.43, D:H.44, D:S.45, D:L.71, D:S.72, D:N.101, D:S.103, D:S.103, D:S.103, D:Y.182, D:K.186, D:S.215, D:L.216 Water bridges: D:R.22, D:G.24, D:N.101, D:S.103 Salt bridges: D:R.21, D:R.22, D:R.22, D:R.43 pi-Cation interactions: D:R.43, D:R.43

4 x MTX: METHOTREXATE(Non-covalent)

MTX.2: 14 residues within 4Å: Chain A: R.22, S.103, Y.105, D.169, L.176, Y.182, G.213, L.214, L.216, P.218, M.221, T.225, Y.229 Ligands: NDP.1 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:L.176, A:P.218 Hydrogen bonds: A:R.22, A:S.103, A:S.103, A:Y.182 Water bridges: A:R.22 pi-Stacking: A:Y.105, A:Y.105, A:Y.229 MTX.4: 14 residues within 4Å: Chain B: R.22, S.103, Y.105, D.169, L.176, F.179, Y.182, L.214, L.216, P.218, M.221, T.225, Y.229 Ligands: NDP.3 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:L.176, B:P.218 Hydrogen bonds: B:R.22, B:S.103, B:S.103, B:Y.182, B:Y.182, B:Y.229 Water bridges: B:Y.105 pi-Stacking: B:Y.105, B:Y.105, B:Y.229 MTX.6: 15 residues within 4Å: Chain C: R.22, S.103, Y.105, D.169, L.176, F.179, Y.182, G.213, L.214, L.216, P.218, M.221, T.225, Y.229 Ligands: NDP.5 11 PLIP interactions: 11 interactions with chain C Hydrophobic interactions: C:L.176, C:P.218 Hydrogen bonds: C:R.22, C:S.103, C:S.103, C:Y.182, C:Y.229 Water bridges: C:T.225 pi-Stacking: C:Y.105, C:Y.105, C:Y.229 MTX.8: 14 residues within 4Å: Chain D: R.22, S.103, Y.105, D.169, L.176, F.179, Y.182, L.214, L.216, P.218, M.221, T.225, Y.229 Ligands: NDP.7 10 PLIP interactions: 10 interactions with chain D Hydrophobic interactions: D:L.176, D:P.218 Hydrogen bonds: D:R.22, D:S.103, D:S.103, D:Y.182, D:Y.182 pi-Stacking: D:Y.105, D:Y.105, D:Y.229

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Schormann, N. et al., Crystal structure of Trypanosoma cruzi pteridine reductase 2 in complex with a substrate and an inhibitor. J.Struct.Biol. (2005)

Release Date

2003-10-14

Peptides

PTERIDINE REDUCTASE 2: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

PTERIDINE REDUCTASE 2

Related Entries With Identical Sequence